PDB Short entry for 5OAB HEADER HYDROLASE 21-JUN-17 5OAB TITLE A NOVEL CRYSTAL FORM OF HUMAN RNASE6 AT ATOMIC RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE K6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 24-150; COMPND 5 SYNONYM: RNASE K6; COMPND 6 EC: 3.1.27.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RNASE6, RNS6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11C KEYWDS RNASE K6, HYDROLASE, PANCREATIC RIBONUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR G.PRATS-EJARQUE,M.MOUSSAOUI,E.BOIX REVDAT 3 17-JAN-24 5OAB 1 LINK REVDAT 2 11-SEP-19 5OAB 1 JRNL REVDAT 1 01-AUG-18 5OAB 0 JRNL AUTH G.PRATS-EJARQUE,J.A.BLANCO,V.A.SALAZAR,V.M.NOGUES, JRNL AUTH 2 M.MOUSSAOUI,E.BOIX JRNL TITL CHARACTERIZATION OF AN RNASE WITH TWO CATALYTIC CENTERS. JRNL TITL 2 HUMAN RNASE6 CATALYTIC AND PHOSPHATE-BINDING SITE JRNL TITL 3 ARRANGEMENT FAVORS THE ENDONUCLEASE CLEAVAGE OF POLYMERIC JRNL TITL 4 SUBSTRATES. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1863 105 2019 JRNL REF 2 SUBJ JRNL REFN ISSN 1872-8006 JRNL PMID 30287244 JRNL DOI 10.1016/J.BBAGEN.2018.09.021 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.PRATS-EJARQUE,J.ARRANZ-TRULLEN,J.A.BLANCO,D.PULIDO, REMARK 1 AUTH 2 M.V.NOGUES,M.MOUSSAOUI,E.BOIX REMARK 1 TITL THE FIRST CRYSTAL STRUCTURE OF HUMAN RNASE 6 REVEALS A NOVEL REMARK 1 TITL 2 SUBSTRATE-BINDING AND CLEAVAGE SITE ARRANGEMENT. REMARK 1 REF BIOCHEM. J. V. 473 1523 2016 REMARK 1 REFN ESSN 1470-8728 REMARK 1 PMID 27013146 REMARK 1 DOI 10.1042/BCJ20160245 REMARK 2 REMARK 2 RESOLUTION. 1.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 54583 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.141 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.680 REMARK 3 FREE R VALUE TEST SET COUNT : 2557 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.7465 - 2.9115 0.99 3111 137 0.1187 0.1359 REMARK 3 2 2.9115 - 2.3109 1.00 3047 149 0.1071 0.1204 REMARK 3 3 2.3109 - 2.0188 1.00 2991 176 0.0903 0.1027 REMARK 3 4 2.0188 - 1.8342 1.00 2985 164 0.0930 0.1281 REMARK 3 5 1.8342 - 1.7027 1.00 3032 123 0.0928 0.1276 REMARK 3 6 1.7027 - 1.6023 1.00 2985 168 0.0894 0.1157 REMARK 3 7 1.6023 - 1.5221 1.00 3003 146 0.0888 0.1349 REMARK 3 8 1.5221 - 1.4558 1.00 2972 161 0.1013 0.1287 REMARK 3 9 1.4558 - 1.3998 0.99 2938 149 0.1054 0.1432 REMARK 3 10 1.3998 - 1.3515 0.99 2990 144 0.1180 0.1729 REMARK 3 11 1.3515 - 1.3092 0.99 3018 114 0.1294 0.1528 REMARK 3 12 1.3092 - 1.2718 1.00 2961 149 0.1420 0.1664 REMARK 3 13 1.2718 - 1.2383 1.00 2974 132 0.1544 0.1978 REMARK 3 14 1.2383 - 1.2081 0.99 2935 166 0.1737 0.1974 REMARK 3 15 1.2081 - 1.1806 0.95 2820 148 0.1983 0.2242 REMARK 3 16 1.1806 - 1.1555 0.90 2660 134 0.2068 0.2559 REMARK 3 17 1.1555 - 1.1324 0.82 2483 103 0.2395 0.2752 REMARK 3 18 1.1324 - 1.1110 0.71 2121 94 0.2798 0.3106 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 1272 REMARK 3 ANGLE : 1.102 1760 REMARK 3 CHIRALITY : 0.099 174 REMARK 3 PLANARITY : 0.008 232 REMARK 3 DIHEDRAL : 13.696 487 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5OAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200004589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : CHANNEL-CUT DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR (CINEL), REMARK 200 CRYOCOOLED, 6MM GAP REMARK 200 OPTICS : VERTICAL FOCUSING MIRROR (VFM) REMARK 200 AND A HORIZONTAL FOCUSING MIRROR REMARK 200 (HFM), MANUFACTURED BY IRELEC REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20151001 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54593 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.111 REMARK 200 RESOLUTION RANGE LOW (A) : 47.703 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08221 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.65560 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.11.1_2575 REMARK 200 STARTING MODEL: 4X09 REMARK 200 REMARK 200 REMARK: CUBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M SODIUM/POTASSIUM PHOSPHATE, PH REMARK 280 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 47.70250 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 47.70250 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 47.70250 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 47.70250 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 47.70250 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 47.70250 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 47.70250 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 47.70250 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 47.70250 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 47.70250 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 47.70250 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 47.70250 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 47.70250 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 47.70250 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 47.70250 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 47.70250 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 47.70250 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 47.70250 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 47.70250 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 47.70250 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 47.70250 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 47.70250 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 47.70250 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 47.70250 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 47.70250 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 47.70250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 327 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 533 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 112 -12.40 89.59 REMARK 500 PRO A 115 45.02 -83.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 607 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A 608 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A 609 DISTANCE = 6.80 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 208 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 1 O REMARK 620 2 TRP A 1 O 2.4 REMARK 620 3 HOH A 474 O 89.1 90.5 REMARK 620 4 HOH A 586 O 124.5 122.7 84.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 209 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 7 O REMARK 620 2 VAL A 121 O 95.8 REMARK 620 3 HOH A 349 O 160.4 102.8 REMARK 620 4 HOH A 521 O 130.2 108.1 37.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 207 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 45 O REMARK 620 2 HOH A 510 O 34.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 213 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 316 O REMARK 620 2 HOH A 361 O 35.0 REMARK 620 3 HOH A 456 O 95.6 87.9 REMARK 620 4 HOH A 514 O 59.2 36.5 52.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 213 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4X09 RELATED DB: PDB REMARK 900 LOWER RESOLUTION X-RAY STRUCTURE OF RNASE 6 USED AS INITIAL REMARK 900 COORDINATES DBREF 5OAB A 1 127 UNP Q93091 RNAS6_HUMAN 24 150 SEQADV 5OAB MET A 0 UNP Q93091 INITIATING METHIONINE SEQRES 1 A 128 MET TRP PRO LYS ARG LEU THR LYS ALA HIS TRP PHE GLU SEQRES 2 A 128 ILE GLN HIS ILE GLN PRO SER PRO LEU GLN CYS ASN ARG SEQRES 3 A 128 ALA MET SER GLY ILE ASN ASN TYR THR GLN HIS CYS LYS SEQRES 4 A 128 HIS GLN ASN THR PHE LEU HIS ASP SER PHE GLN ASN VAL SEQRES 5 A 128 ALA ALA VAL CYS ASP LEU LEU SER ILE VAL CYS LYS ASN SEQRES 6 A 128 ARG ARG HIS ASN CYS HIS GLN SER SER LYS PRO VAL ASN SEQRES 7 A 128 MET THR ASP CYS ARG LEU THR SER GLY LYS TYR PRO GLN SEQRES 8 A 128 CYS ARG TYR SER ALA ALA ALA GLN TYR LYS PHE PHE ILE SEQRES 9 A 128 VAL ALA CYS ASP PRO PRO GLN LYS SER ASP PRO PRO TYR SEQRES 10 A 128 LYS LEU VAL PRO VAL HIS LEU ASP SER ILE LEU HET PO4 A 201 5 HET PO4 A 202 5 HET PO4 A 203 10 HET PO4 A 204 5 HET PO4 A 205 10 HET PO4 A 206 5 HET NA A 207 1 HET NA A 208 1 HET NA A 209 1 HET CL A 210 1 HET CL A 211 1 HET CL A 212 1 HET K A 213 1 HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM K POTASSIUM ION FORMUL 2 PO4 6(O4 P 3-) FORMUL 8 NA 3(NA 1+) FORMUL 11 CL 3(CL 1-) FORMUL 14 K K 1+ FORMUL 15 HOH *309(H2 O) HELIX 1 AA1 THR A 6 ILE A 16 1 11 HELIX 2 AA2 GLN A 22 GLN A 35 1 14 HELIX 3 AA3 SER A 47 CYS A 55 1 9 SHEET 1 AA1 4 GLN A 40 LEU A 44 0 SHEET 2 AA1 4 VAL A 76 SER A 85 -1 O CYS A 81 N ASN A 41 SHEET 3 AA1 4 ARG A 92 ASP A 107 -1 O ARG A 92 N THR A 84 SHEET 4 AA1 4 CYS A 69 GLN A 71 -1 N HIS A 70 O VAL A 104 SHEET 1 AA2 4 GLN A 40 LEU A 44 0 SHEET 2 AA2 4 VAL A 76 SER A 85 -1 O CYS A 81 N ASN A 41 SHEET 3 AA2 4 ARG A 92 ASP A 107 -1 O ARG A 92 N THR A 84 SHEET 4 AA2 4 VAL A 119 LEU A 127 -1 O VAL A 121 N ALA A 105 SSBOND 1 CYS A 23 CYS A 81 1555 1555 2.05 SSBOND 2 CYS A 37 CYS A 91 1555 1555 2.05 SSBOND 3 CYS A 55 CYS A 106 1555 1555 2.07 SSBOND 4 CYS A 62 CYS A 69 1555 1555 2.05 LINK O ATRP A 1 NA NA A 208 1555 1555 2.82 LINK O BTRP A 1 NA NA A 208 1555 1555 2.64 LINK O LYS A 7 NA NA A 209 1555 1555 2.83 LINK O HIS A 45 NA NA A 207 1555 22454 3.01 LINK O VAL A 121 NA NA A 209 1555 1555 2.68 LINK NA NA A 207 O AHOH A 510 1555 1555 3.04 LINK NA NA A 208 O HOH A 474 1555 1555 2.78 LINK NA NA A 208 O HOH A 586 1555 1555 2.79 LINK NA NA A 209 O HOH A 349 1555 1555 2.99 LINK NA NA A 209 O HOH A 521 1555 1555 2.82 LINK K A K A 213 O HOH A 316 1555 1555 2.82 LINK K A K A 213 O HOH A 361 1555 1555 3.16 LINK K A K A 213 O AHOH A 456 1555 1555 2.66 LINK K A K A 213 O HOH A 514 1555 1555 3.42 CISPEP 1 TYR A 88 PRO A 89 0 7.43 SITE 1 AC1 10 LYS A 3 ARG A 4 LYS A 100 HOH A 312 SITE 2 AC1 10 HOH A 329 HOH A 334 HOH A 341 HOH A 359 SITE 3 AC1 10 HOH A 468 HOH A 475 SITE 1 AC2 9 HIS A 15 HIS A 122 LEU A 123 CL A 211 SITE 2 AC2 9 HOH A 311 HOH A 345 HOH A 348 HOH A 349 SITE 3 AC2 9 HOH A 434 SITE 1 AC3 5 HIS A 36 HIS A 39 LYS A 87 HOH A 303 SITE 2 AC3 5 HOH A 305 SITE 1 AC4 4 ARG A 92 HOH A 315 HOH A 399 HOH A 406 SITE 1 AC5 9 ARG A 66 HIS A 67 ASN A 68 HOH A 301 SITE 2 AC5 9 HOH A 307 HOH A 314 HOH A 318 HOH A 326 SITE 3 AC5 9 HOH A 470 SITE 1 AC6 2 ASN A 24 ARG A 92 SITE 1 AC7 5 TRP A 1 LYS A 7 PRO A 18 HIS A 45 SITE 2 AC7 5 CL A 210 SITE 1 AC8 5 MET A 0 TRP A 1 TYR A 99 HOH A 474 SITE 2 AC8 5 HOH A 586 SITE 1 AC9 5 LYS A 7 VAL A 121 CL A 211 HOH A 349 SITE 2 AC9 5 HOH A 521 SITE 1 AD1 4 HIS A 122 NA A 207 HOH A 309 HOH A 500 SITE 1 AD2 5 PHE A 11 GLN A 14 HIS A 15 PO4 A 202 SITE 2 AD2 5 NA A 209 SITE 1 AD3 6 LYS A 7 PRO A 20 GLN A 110 K A 213 SITE 2 AD3 6 HOH A 346 HOH A 553 SITE 1 AD4 5 PRO A 20 GLN A 110 CL A 212 HOH A 316 SITE 2 AD4 5 HOH A 456 CRYST1 95.405 95.405 95.405 90.00 90.00 90.00 I 2 3 24 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010482 0.00000